Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers

The present study, using RAPD analysis, was undertaken to characterize genetic variation in domesticated cowpea and its wild progenitor, as well as their relationships. The materials used consisted of 26 domesticated accessions, including accessions from each of the five cultivar-group, and 30 wild/weedy accessions, including accessions from West, East and southern Africa. A total of 28 primers generated 202 RAPD bands. One hundred and eight bands were polymorphic among the domesticated compared to 181 among wild/weedy cowpea accessions. Wild accessions were more diverse in East Africa, which is the likely area of origin of V. unguiculata var. spontanea. Var. spontanea is supposed to have spread westward and southward, with a loss of variability, loss counterbalanceed in southern Africa by introgressions with local perennial subspecies. Although the variabilty of domesticated cowpea was the highest ever recorded, cultivar-groups were poorly resolved, and several results obtained with isozyme data were not confirmed here. However primitive cultivars were more diverse than evolved cultivars, which still suggests two consecutive bottlenecks within domesticated cowpea evolution. As isozymes and AFLP markers, although with a larger number of markers, RAPD data confirmed the single domestication hypothesis, the gap between wild and domesticated cowpea, and the widespread introgression phenomena between wild and domesticated cowpea.     

Evidence for two gene pools of the Lima bean,Phaseolus lunatus L., in the Americas

Summary The lima bean,Phaseolus lunatus L., is a bean species with a broad distribution in the Americas that rivals that of common bean (P. vulgaris). In order to better understand the organization of genetic diversity and the pattern of domestication in lima bean, a review was conducted of the available information on the geographic distribution of wild and cultivated forms of this species. In addition, one-dimensional SDS polyacrylamide gel electrophoresis of seed proteins was also conducted on a sample of 84 wild, 6 weedy, and 426 cultivated forms. Results show that wild forms can be divided into two groups, one with smaller seeds and a very extensive distribution that includes Mexico, Central America, and the eastern slope of the Andes, and the other with a more circumscribed distribution on the western slope of the Andes in Ecuador and northern Peru. Electrophoretic analyses of seed proteins confirmed this subdivision and, additionally, showed that the large-seeded cultivars had been domesticated from the large-seeded wild lima beans in western South America. For the small-seeded lima bean cultivars, it was not possible to determine a domestication center as the most abundant protein pattern in the cultivars also had a widespread distribution in the small-seeded wild progenitor. Electrophoretic analyses showed, however, that domestication led to a reduction of genetic diversity in the small-seeded, Mesoamerican group, but not in the large-seeded group. The latter may be due to insufficient sampling of the larger-seeded, wild germplasm.     

Genetic Structure of Wild and Domesticated Populations of Capsicum annuum (Solanaceae) from Northwestern Mexico Analyzed by RAPDs

Levels of genetic variation and genetic structure of 15 wild populations and three domesticated populations of Capsicum annuum were studied by RAPD markers. A total of 166 bands (all of them polymorphic) and 126 bands (125 of them polymorphic) were amplified in wild and domesticated populations, respectively. Mean percentage of polymorphism was 34.2% in wild populations and 34.7% in domesticated populations. Mean and total genetic diversity were 0.069 and 0.165 for wild populations and 0.081 and 0.131 for domesticated populations. Parameters of genetic diversity estimated from 54 bands with frequencies ≥1 − (3/n) (n = sample size) showed that 56.7% of the total variation was within and 43.3% among wild populations, whereas 67.8% of the variation was within and 32.2% among domesticated populations. AMOVA indicated that total genetic diversity was equally distributed within (48.9 and 50.0%) and among (50.0 and 51.1%) populations in both wild and domesticated samples. Wild and domesticated populations were clearly resolved in a UPGMA dendrogram constructed from Jaccard’s distances (average GD = 0.197), as well as by AMOVA (17.2% of variance among populations types, p = 0.001) and by multidimensional scaling analysis. Such differentiation can be associated with domestication as well as different origin of gene pools of the wild (Northwestern Mexico) and cultivated (more probably Central Mexico) samples analyzed. The considerable genetic distances among cultivars (average GD = 0.254) as well as the high number of diagnostic bands per cultivar (33 out of 126 bands), suggest that genetic changes associated with domestication could have resulted from artificial selection intervening in different directions, but the inclusion of more domesticated samples might clarify the nature of distinctions detected here.     

Yam (Dioscorea ssp.) domestication by the Nago and Fon ethnic groups in Benin

Guinea yams (Dioscorea cayenensis-rotundata complex; D. rotundata Poir. and D. cayenensis Lam.) have been described as resulting from a process of domestication of wild yams of the section Enantiophyllum by African farmers. Although currently practised by few farmers, the process of yam domestication is still on-going in Benin. In order to document the practices used and the indigenous knowledge maintained by Nago and Fon farmers, 27 villages were surveyed. In total, 57 farmers domesticating yam were identified, and 68 yams newly domesticated (or in domestication) were collected. Fon and Nago farmers domesticate yam mainly to widen the genetic basis of the existing diversity or for simple curiosity. Among the three wild yams species (D. abyssinica Hochst. ex Kunth, D. praehensilis Benth. and D. burkilliana J. Miège) used, D. praehensilis is the most important and the most exploited. Tuber of the wild yams are collected either in the bush (most often near the village) or in the forests (far from the village) during hunting. The domestication process consists of bringing into cultivation selected individuals which go through intense vegetative multiplication and selection procedures (over a lengthy but variable period of time) that induce morphological and biochemical changes in the plant mainly at the tuber level. Individuals resulting from these manipulations were found to be, either similar or identical to known landraces or completely new based on both morphological and isozyme analysis. Because it leads to some new cultivars, this process of domestication has potential in yam breeding and appears to be a strategy that could be useful to breeders, while developing a methodology for participatory breeding of yam.     

Primitive weedy forms of guar,adak guar: possible missing link in the domestication of guar [<Emphasis Type="Italic">Cyamopsis tetragonoloba</Emphasis> (L.) Taub.]

Crop domestication has lead to the selection of a wide range of traits that distinguish domesticated crops from their wild ancestors. Over the past four decades, concerted efforts by archaeologists and geneticists have provided novel insights into the domestication of crops. However, minor crops are rarely a subject for intensive domestication studies and very less is known on the domestication of guar [Cyamopsis tetragonoloba (L.) Taub.] except the trans-domestication hypothesis. The hypothesis proposes that the domestication of guar took place in recent times in the dry areas of the northwestern region of Indo-Pakistan subcontinent and the African wild species, C. senegalensis Guill. et Perr., as its ancestor. However, the process by which the wild species was domesticated is not fully understood. The present paper describes the exploration, collection and in situ characterization of the primitive weedy forms of guar that could be the missing link between the wild and cultivated species. Adak guar is found to grow along with cultivated guar as a weed and is characterized by several primitive characters, prominent among which are spreading habit, small inedible pods which shatter at maturity, hard seed coat and seed dormancy. A total of 66 germplasm collections of these primitive weedy forms of guar have been made from naturally occurring populations in the arid regions of northwestern India. Systematic studies involving these primitive weedy forms can help in understanding the domestication bottlenecks and in utilizing the genetic variation lost during the process of domestication for the improvement of cultivated guar.     

Genetic diversity among varieties of Chia (Salvia hispanica L.)

Chia, Salvia hispanica L., was a staple crop in pre-Columbian Mesoamerica. Despite the great potential of the species as an oilseed crop, little research related to domesticated and wild varieties exists. A study was undertaken to assess genetic diversity among 38 wild and domesticated accessions of S. hispanica collected throughout Mesoamerica by using RAPD markers. Genetic diversity was higher among wild varieties (H _G= 0.15) than all domesticated varieties (H _G= 0.10) and modern commercial domesticated varieties (H _G= 0.02), suggesting a slight loss of diversity accompanying domestication and a near lack of diversity in modern commercial varieties. In addition, the preliminary results indicate that the center of genetic diversity is in the highlands of western Mexico.     

The fragrance (fgr) gene in natural populations of wild rice (Oryza rufipogon Griff.)

The Asian cultivated rice, Oryza sativa L. (spp. indica or japonica), is assumed to have originated from one or both of the two wild Asian species, O. rufipogon Griff. and O. nivara Sharma and Shastry. They occur throughout the monsoon Asia and west Oceania. Fragrance is the most important trait among the domesticated characters of basmati and jasmine rice of Asia. The gene for fragrance in a scented rice shows the presence of a mutated portion (i.e., an eight base pair deletion in exon 7) that result in its loss of fragrance. In the present study, 229 wild rice O. rufipogon accessions were genotyped for this locus using a PCR assay. The wild rice species contained the mutated allele of the fgr gene at a low frequencies of 0.23. The surveyed populations were in Hardy–Weinberg equilibrium. This observation supports the hypothesis that the allele for fragrance was already present in the wild rice, and that this trait appeared in scented rice cultivars because of selection by the farmers of genotypes possessing this character during the process of domestication.     

Origin and ancestry of Egyptian clover (<Emphasis Type="Italic">Trifolium alexandrinum</Emphasis> L.) As revealed by AFLP markers

The origin and ancestry for Egyptian clover, Trifolium alexandrinum, was examined using AFLP data. The data support a close relationship of T. alexandrinum accessions from Syria and Egypt to T. apertum, T. berytheum, and T. salmoneum. However, crossability and geographic distributions suggest that T. apertum is an unlikely progenitor. In contrast, T. salmoneum appears to be the most probable progenitor for Syrian material of Egyptian clover, although a close relationship to T. berytheum was also revealed. The ability of these species to cross freely indicates that T. salmoneum and T. berytheum may be regarded as the primary ancestors from, which man domesticated Egyptian clover through artificial selection in Syria. Following domestication, the earlier forms of the crop species could have been taken into rain-fed cultivation in Palestine and irrigated cultivation in Egypt. In this regard, the domestication of Egyptian clover may be analogous to other crops, such as barley and wheat, which were also domesticated in the Fertile Crescent and taken into cultivation in the Nile Valley. It appears that genetic improvement of the crop occurred in Egypt after cultivation, and that the varieties that were developed in Egypt were later distributed worldwide.     

Genetic diversity and population structure of Capsicum baccatum genetic resources

Capsicum baccatum is one of five domesticated pepper species which, despite its morphological and ecological variability, has been underexploited for germplasm improvement. Utilizing a broad spectrum of domesticated and wild C. baccatum germplasm, we utilize AFLP markers to describe the species’ molecular diversity and population structure in the South American gene pool. Analysis of molecular variance (AMOVA) revealed greater genetic diversity in the wild form of C. baccatum (C. baccatum var. baccatum) than in the domesticated form of the species (C. baccatum var. pendulum). Both Bayesian and distance based clustering analysis, as well as principal coordinates analysis (PCA), concordantly demonstrated admixture/shared ancestry between wild and cultivated C. baccatum botanical varieties. Two principal genetic groups were identified in the domesticated C. baccatum accessions largely based on their geographic distribution in South America. One group was predominated by accessions from the western territories of the species’ distribution (Peru, Colombia, Ecuador, Bolivia, Chile and northwestern Argentina) and the second by accessions from the eastern regions, Paraguay and eastern Argentina). The two genetic groups overlapped in the geographic location of present-day Bolivia. The grouping pattern suggested that C. baccatum was domesticated in multiple sites and that its evolution took two lineages followed by lineage differentiation. The wild accessions most closely related to the cultigens were found in the highlands of Peru and Bolivia, which support the early hypothesis that this region is one of the domestication sites of this species. A Bayesian assignment analysis demonstrated that Brazilian wild forms of C. baccatum were genetically distant to all other accessions and made little to no contribution to the domesticated genepool. Moreover, results of clustering analysis suggested that C. baccatum likely originated from present day Paraguay. Analysis of inter-specific relationships across selected Capsicum species supported independent lineages for the two crossability groups within Capsicum, the baccatum species-complex (including C. baccatum) and the annuum species-complex (including C. annuum, C. chinense and C. frutescens). However, the results did not support taxonomic distinction of C. baccatum var. umbilicatum from C. baccatum var. pendulum. The present study provides new insights into the domestication of C. baccatum. The results will be useful for identifying accessions for crop improvement and guiding the development of in situ and ex situ conservation programs.     

Determining Sources of Diversity in Cultivated and Wild <Emphasis Type="Italic">Lablab purpureus</Emphasis> Related to Provenance of Germplasm by using Amplified Fragment Length Polymorphism

To improve understanding of diversity of Lablab purpureus and establish relationships among 103 germplasm accessions collected from diverse geographic origins, amplified fragment length polymorphism markers were used. Four primer sets selected out of 16 produced 289 clear, repeatable polymorphisms. UPGMA analysis of similarity data clustered the accessions according to their subspecific taxonomic organization, i.e., subsp. purpureus and subsp. uncinatus, as well as to cultivated and wild forms. The well-represented landraces from Africa and Asia, belonging predominantly to subsp. purpureus, displayed moderate genetic diversity. Wild forms from Africa showed far greater levels of diversity that would justify taxonomic re-assessment of the wild subsp. uncinatus. The molecular analysis identified forms that were collected in the wild in India but were genetically placed intermediate between wild and cultivated forms. As these plant types did not exist among the African accessions, it is suggested that they might represent escapes from early attempts of domestication. These results support the suggested pathway of domestication and distribution of L. purpureus from Africa to Asia. Additional members to a previously published core collection of the species are proposed.     

Genetic identity and relationships of Iranian apple (Malus?×?domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis

In order to shed light on the role of Iran in apple evolution and domestication, we chose to investigate the relationships of a collection of 159 accessions of wild and domesticated apples including Iranian indigenous apple cultivars and landraces, selected wild species, and old apple scion and rootstock cultivars from different parts of the world. The majority of the wild species belonged to M. sieversii, which is widely believed to be the main maternal wild ancestor of domestic apples, from Kazakhstan and M. orientalis, which is one of the probable minor ancestors of domestic apples, from Turkey and Russia located on the east and west of Iran, respectively. The accessions were assigned into six arbitrary populations for the purpose of generating information on genetic parameters. Nine simple sequence repeat (SSR) loci selected from previous studies in apple were screened over DNA extracted from all the accessions. Results showed that all SSR loci displayed a very high degree of polymorphism with 11–25 alleles per locus. In total, there were 153 alleles across all loci with an average of 17 alleles per locus. The SSR allelic data were then used for estimation of population genetic parameters, including genetic variation statistics, F-statistics, gene flow, genetic identity, genetic distance and then cluster analysis using POPGENE 1.32 software. The F-statistics and gene flow in particular, showed that there was more intra-population than between population variation. The genetic identity and genetic distance estimates, and the dendrogram generated from the un-weighted pair group arithmetic average (UPGMA) method of cluster analysis showed that the Iranian cultivars and landraces were more closely related to M. sieversii from Central Asia (east of Iran) and M. orientalis native to Turkey and Russia than to other accessions of Malus species. Also, the old apple cultivars from different parts of the world have a closer genetic relationship to M. sieversii, M. orientalis and the Iranian apples, than to other wild species. Based on these results, we suggest that the Iranian apples may occupy an intermediate position between the domesticated varieties and wild species. We propose that Iran could be one of the major players in apples’ domestication and transfer from Central Asia to the western countries.     

Exogenous Spermidine Affected Leaf Characteristics and Growth of Common Bean Under Water Deficit Conditions

In order to investigate the effects of exogenous spermidine on water limitation-induced damage on common bean (Phaseolus vulgaris L.) genotypes, a field experiment was conducted over two growth seasons. The experiment was arranged as a split-split plot design and three replications. Treatments were three water stress levels (non-stress, moderate and severe stress), three bean genotypes (Akhtar, Pak and COS12) and two spermidine levels (control and foliar application). The results showed that water stress reduced markedly leaf relative water content, SPAD values, specific leaf area, leaf area index, plant height, relative growth rate, shoot dry weight and grain yield; however, increased leaf density, leaf relative electrolyte leakage, stomatal density, leaf angle and leaf temperature of bean genotypes. Spermidine application increased relative water content, SPAD values, leaf area, leaf area index, shoot dry weight and grain yield. Overall, exogenous spermidine usage as a free radical scavenger counteracted deleterious water deficit effects.     

Observations on the geographic distribution, ecology and conservation status of several Phaseolus bean species in Costa Rica

Interest in bean genetic resources of Central America has resumed because of disease pressures (e.g., web blight, BGMV) and limitations of current bean varieties. As most of the diversity in landraces has been explored, focus is now on the exploration of wild forms of the primary gene pool and wild species of the secondary gene pool. A germplasm collection was carried out in the field and resulted in the collection of 29 wild populations for six Phaseolus species; it complemented field work done in 1987. Nine more populations were found for P. costaricensis, 10 for wild P. lunatus, one for P. oligospermus, one for P. tuerckheimii, four for wild P. vulgaris and four for P. xanthotrichus. Ninety-three herbarium voucher specimens were collected for 19 populations of the six species (deposited at CR). These results confirm the presence of wild P. vulgaris on both slopes of the central valley of Costa Rica, namely in the life zones bh-MB and bmh-P, and of P. costaricensis in the life zone bmh-MB. These life zones of limited range in Costa Rica have been heavily modified, thus fully justifying the germplasm collection for ex situ conservation. For both species the range of distribution in Costa Rica has been almost completely sampled. The life characteristics of each species that are relevant for their conservation in situ are briefly reviewed. Distribution ranges of each wild bean species are compared with the present extension of national parks, protected areas and fauna/flora sanctuaries, and suggestions for expanding such protected areas are made.     

Stomatal frequency and size differentiate ploidy levels in Aegilops neglecta

Aegilops neglecta Req. ex Bertol. is a forage goatgrass that has tetraploid and hexaploid forms. No morphological trait is known to distinguish between the two forms. Accessions of Ae. neglecta representing diverse germplasm were characterized for stomatal frequency and size on the adaxial surface of leaves. Stomatal frequency among tillers within a plant and among leaves on a tiller was measured. Significant variation was found in stomatal frequency between the ploidy levels for basal leaves 2 and 3 and the penultimate and flag leaves. Mean stomatal frequency for basal leaves ranged from 50.24 to 54.80 per mm² for tetraploid and from 39.24 to 40.50 per mm² for hexaploid accessions. For upper leaves, it varied from 52.88 to 53.50 per mm² for tetraploid and from 46.12 to 46.40 per mm² for hexaploid accessions. The two ploidy forms also exhibited clear differences for stomatal size on the basal and upper leaves of the main tiller. Mean stomatal size for the basal leaves ranged from 41.42 to 46.09 m for tetraploid and from 53.59 to 54.97 m for hexaploid accessions. For upper leaves, stomatal size varied from 47.29 to 53.29 m in tetraploid and from 64.76 to 66.84 m for hexaploid accessions. None of the individual accession ranges overlapped between the ploidy levels. Stomatal frequency and size were highly negatively correlated. Increased ploidy in Ae. neglecta has resulted in fewer but larger stomata per unit leaf area. Stomatal size and/or frequency on the adaxial surface of leaves could be used to distinguish tetraploid from hexaploid cytotypes in Ae. neglecta in fresh material from Turkey collected in the field.     

鄂尔多斯高原沙地柏液流通量及其影响因子

[目的]分析沙地柏液流通量变化特征及主要影响因子,为沙地植被的保护提供理论依据。[方法]以鄂尔多斯高原沙地植被的优势种沙地柏为研究对象,利用热扩散(TDP)技术监测生长季沙地柏的液流动态,通过相关分析和回归分析等研究其与气象因子的关系。[结果]晴天沙地柏的液流通量为单峰曲线,干旱时为双峰曲线。雨天沙地柏的液流通量为单峰或双峰曲线。晴天沙地柏液流通量的最大值是2.30～23.38 g/(cm~2·h)。沙地柏液流通量对降雨的响应具有1～4 d的时滞。生长季沙地柏液流通量与光合有效辐射、水汽压亏缺、气温和风速均呈显著正相关,而与相对湿度和降雨量呈显著负相关。[结论]鄂尔多斯高原沙地柏的液流通量随天气而变化。太阳辐射和水分是沙地柏液流通量的主要影响因子。建议当地加强对沙地柏灌丛的保护,防止由于过度水分消耗导致的植被退化。     

Diversity of native rice (Oryza Poaceae:) species of Costa Rica

We found several populations of wild Oryza species in the lowlands of Costa Rica. The plants showed extensive morphological variation, suggesting the presence of several species. In the morphologic study, 33 traits were scored for plants of all the species. A principal component analysis revealed the significant morphological separation of the different species. The analyses indicated that there are three species, O. grandi­glumis, O. latifolia and O. glumaepatula. Two putative hybrid types were found, both significantly differing in their morphology from the known species and intermediate at several traits. O. grandi­glumis is a new record for Costa Rican flora. Its main population is located in Caño Negro Wildlife Refuge, Los Chiles, Alajuela. O. latifolia is distributed throughout the lowlands of the country and the plants of the Atlantic slope are significantly bigger in general habit than those of the Guanacaste area. During this study a population of O. glumaepatula of hundreds of thousands of plants was discovered in the Medio Queso River wetland, Los Chiles, Alajuela. This population is the most important source of genes for cultivar's improvement from the primary gene pool of rice in Costa Rica. The small ligule and the wide flag leaf characteristic of the two CCDD species separated them from the AA diploid O. glumaepatula. Seed size, ligule size, number of branches in the panicle, plant height and sterile lemma length are all bigger in O. grandi­glumis, and influenced the second factor that separated the CCDD species in two discrete clusters. The species found offer great possibilities for the improvement of rice cultivars and they should be thoroughly studied and appropriately protected.     

土壤干旱下氮磷营养对玉米气体交换的影响

在盆栽条件下就氮磷营养对玉米叶片气体交换的影响进行了比较研究。结果发现 :虽然土壤干旱条件下 ,氮磷均增大了玉米叶片的气孔导度 ,但氮对促进干旱条件下气孔开放的作用要显著大于磷的作用 ;土壤干旱条件下 ,氮磷均有增大玉米叶片光合速率的作用 ,但氮有同时减小光合的气孔和非气孔限制的作用 ,而磷提高干旱条件下的光合速率则主要以减小光合的非气孔限制 (提高叶肉光合活性 )为主 ;由于氮磷对玉米叶片气孔导度和光合作用的不同影响 ,因而表现出其在提高干旱条件下玉米叶片水分利用效率方面的不同作用 ,其中磷对提高干旱条件下玉米水分利用效率的作用更为明显     

The domestication and dispersal of the cultivated ramie (Boehmeria nivea (L.) Gaud. in Freyc.) determined by nuclear SSR marker analysis

Ramie (Boehmeria nivea) was domesticated in China. However, the geographic region of domestication is not exactly known. Genetic diversity and population structure of ramie and their wild relatives were assessed using microsatellite markers. The 8 microsatellite primers revealed 96 alleles in 50 ramie populations, with an average of 10.25 alleles per locus. Cultivated ramie gene pool harbors approximately 82.9 % of the SSR diversity presented in wild B. nivea var. nivea. It is suggested that ramie has experienced a relatively moderate domestication bottleneck. The distribution of genetic diversity shows that genetic diversity is relatively high in populations along the Yangtze River compared to the peripheral ones. The scatter plots of principal coordinates analysis indicated that there are three well-supported varieties in B. nivea. The NJ tree and the distribution of genetic diversity showed that ramie has been domesticated in the middle and lower regions of the Yangtze valley, and populations in Sichuan province have been introduced from this region, forming naturalized populations.     

Multivariate analysis of phenotypic diversity of Coffea arabica

Summary Eighteen different morphological and agronomical traits observed in a field collection of 148 accessions of Coffea arabica were analyzed using multivariate analysis. For the first time, a clear structure is observed within this species with the identification of two main groups. Accessions of group 1 have a more erect branching habit, narrower leaves and are on average more resistant to coffee leaf rust and coffee berry disease than accessions of group 2. Group 1 mostly contains Ethiopian accessions collected west of the Great Rift Valley, whereas group 2 mostly contain commonly cultivated varieties throughout the world and Ethiopian accessions collected east of the Great Rift Valley in Ethiopia. This phenotypic structure together with historical evidence suggest that group 1 has not been involved in the domestication of C. arabica. The present results confirm that sub-spontaneous genotypes west of the Rift Valley are highly valuable for enriching the genetic basis of cultivated C. arabica germplasm. The potential value of this material in breeding of C. arabica is discussed.